Significant Parent-of-Origin Effects for Seed, Cotyledon, and Early Plant Growth Traits in Cucumber

Round 1

Reviewer 1 Report

To evaluate the parent-of-origin effects on seed, cotyledon, and early growth traits in cucumber, the authors generate 56 hybrids by crossing two doubled haploids (DHs) extracted from each of four cucumber populations in a full diallel mating scheme under the controlled growth conditions. The authors found a significant correlation among seed traits, cotyledon leaf length, and the weight of early growth seedlings, as well as the signification variation in General Combining Ability (GCA), Specific Combining Ability (SCA), and Reciprocal effects for all quantified traits. The authors did the RNA-seq by collecting samples from two sets of reciprocal hybrids with significant/non-significant reciprocal effects. Transcriptome analysis among the reciprocal DH hybrids revealed the sets of significantly differentially expressed genes (DEGs) across various functional categories. The experiment design and data analysis are clear and reveal the reciprocal crossing for improving the cucumber hybrid development. There are some questions listed as following:

1. Cucumber has a maternal inheritance of the chloroplast and paternal inheritance of the mitochondria. How many DEGs from reciprocal crosses of DH hybrids are cytoplasmic parent-of-origin effect genes? Are the genes Csa7G368160 and Csa5G623470 the parent-of-origin effect genes?
2. Are there some reported homolog imprinting genes of other species, such as Arabidopsis, maize, and rice from the list of the significant DEGs,?
3. What are the significant general combining ability (GCA), specific combining ability (SCA), and reciprocal effects? Please explain in the Introduction or the Materials and Methods.
4. Suggest summarizing the GO term analysis in one figure, and putting Table 6 and Table 7 in the supplementary part.

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Crossings to make hybrids is exploited to increase performance of many crop species. This manuscript report on parent-of-origin effects on cucumber populations used in reciprocal crosses. Using four populations, each with two individual double haploid (DH) lines the authors show by reciprocal crosses that hybrid traits are dependent on cross direction. The authors evaluated seed size, cotyledon size as well as fresh and dry weight of 20 days old plant to evaluate the performance of 56 hybrid crosses. RNA sequencing analysis was further included to identify common patterns of gene expression in hybrids with significant reciprocal effects.

A list of suggestions and major and minor concerns follows below:

Major:

Reference 61. Olberg PhD. I assume the work of this thesis has not been published in any peer reviewed journals. I can also not find it anywhere. If it is available electronically this should be stated somewhere, as the reference to this work is quite extensively used in this current manuscript. Current manuscript is also referring to specific data in the Olberg reference. You should consider keeping those tables as supplementary material to the current MS or at least make the data available according to MDPI Agronomy Instructions to Authors https://www.mdpi.com/journal/agronomy/instructions#suppmaterials

Minor:

Lines95-99: Missing definition of general and specific combining ability.

Line105: SSR. what is it an abbreviation of?

Line108-110: How many seeds per fruit or total n seeds?

Line 135: Formatting- brackets around references.

Lines 136-143: formatting of equations: references to crosses and experiments (i-j-k-l) subscript will greatly enhance the readability of this section. Y_ijkl

Line 145: SAS- abbreviation for?

Line 279: spelling? similarity

Line 522: two references with same number (number 52). this and all later references needs to be updated in reference list and text.

Table 5: Formatting: Panels are not consistent with each other regarding lines and highlighted cell borders.

Table 6: Suggest to condense Table,

Author Response

Please see the attachment.

Author Response File: Author Response.pdf